For me, it's not for being the main character, but is given such high treatment when he really didn't do anything to deserve it.
The Destroy Gundam, frankly, failed in all aspects EXCEPT when it involved two "key" characters (Shinn and Stellar). As soon as Stellar was out of the picture, the Destroy Gundam was no better than most other grunt units when it came to Shinn (and Rey), even though one of the five used at Orb was being piloted by another Extended just like her (Sting). By all common sense, that should mean it should've put up just as much if not more of a fight than Stellar's one single one did, but nope...all five taken out like nothing (and three more on the moon).
As for Athrun, he may have destroyed the Strike, but it cost him the Aegis as well because it ran out of power and left him no other choice but to self-destruct it if he wanted to kill Kira at the time so that battle can only be called a tie at best.
For the Impulse...well...no one could really expect someone as underused as Lunamaria to be able to defeat Athrun. If it were still Shinn or someone else actually "important" (to the directors and such anyway), chances are it would've performed better (but still lose).
For the Destiny, it wasn't just Athrun and SEED Mode (it did play a role, but it wasn't the only factor), but also partly due to Shinn just losing his head over Lunamaria getting knocked out by Athrun and not thinking straight unlike his fight against Kira and the Freedom where he planned ahead of time while studying Kira's fighting tactics, and used all the Silhouette Packs at his disposal and even creatively used the Core Splendor construction to dodge one of Kira's strikes.
If the director actually stuck with Shinn and properly developed him, as well as the plot and such in general, who knows what he could've been able to do. Unfortunately, what the director and others did can't be undone and Shinn will forever be seen as one of if not the worst Gundam "protagonist" in the franchise.
